Search Results - Nathan C. Sheffield

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  1. 1
    LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

    LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor by Nathan C. Sheffield, Christoph Bock

    Published 2015
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  2. 2
    Multi-Omics of Single Cells: Strategies and Applications

    Multi-Omics of Single Cells: Strategies and Applications by Christoph Bock, Matthias Farlik, Nathan C. Sheffield

    Published 2016
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  3. 3
    ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

    ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors by Christian Schmidl, André F. Rendeiro, Nathan C. Sheffield, Christoph Bock

    Published 2015
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  4. 4
    Opportunities and challenges in sharing and reusing genomic interval data

    Opportunities and challenges in sharing and reusing genomic interval data by Bingjie Xue, Oleksandr Khoroshevskyi, R. Ariel Gómez, Nathan C. Sheffield

    Published 2023
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  5. 5
    A Comparative Analysis of Mitochondrial Genomes in Coleoptera (Arthropoda: Insecta) and Genome Descriptions of Six New Beetles

    A Comparative Analysis of Mitochondrial Genomes in Coleoptera (Arthropoda: Insecta) and Genome Descriptions of Six New Beetles by Nathan C. Sheffield, Hojun Song, Stephen L. Cameron, Michael F. Whiting

    Published 2008
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  6. 6
    Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics

    Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics by Nathan C. Sheffield, Hojun Song, Stephen L. Cameron, Michael F. Whiting

    Published 2009
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  7. 7
    GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA

    GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA by Oleksandr Khoroshevskyi, Nathan J. LeRoy, Vincent Reuter, Nathan C. Sheffield

    Published 2023
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  8. 8
    Predicting cell-type–specific gene expression from regions of open chromatin

    Predicting cell-type–specific gene expression from regions of open chromatin by Anirudh Natarajan, Galip Gürkan Yardımcı, Nathan C. Sheffield, Gregory E. Crawford, Uwe Ohler

    Published 2012
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  9. 9
    Refgenie: a reference genome resource manager

    Refgenie: a reference genome resource manager by Michał Stolarczyk, Vincent Reuter, Jason P. Smith, Neal E. Magee, Nathan C. Sheffield

    Published 2020
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  10. 10
    Mitochondrial genomics in Orthoptera using MOSAS

    Mitochondrial genomics in Orthoptera using MOSAS by Nathan C. Sheffield, Kevin D. Hiatt, Mark C. Valentine, Hojun Song, Michael F. Whiting

    Published 2010
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  11. 11
    Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

    Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics by Matthias Farlik, Nathan C. Sheffield, Angelo Nuzzo, Paul Datlinger, Andreas Schönegger, Johanna Klughammer, Christoph Bock

    Published 2015
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  12. 12
    BART: a transcription factor prediction tool with query gene sets or epigenomic profiles

    BART: a transcription factor prediction tool with query gene sets or epigenomic profiles by Zhenjia Wang, Mete Civelek, Clint L. Miller, Nathan C. Sheffield, Michael J. Guertin, Chongzhi Zang

    Published 2018
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  13. 13
    PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments

    PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments by Jason P. Smith, M. Ryan Corces, Jin Xu, Vincent Reuter, Howard Y. Chang, Nathan C. Sheffield

    Published 2021
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  14. 14
    Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

    Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions by Nathan C. Sheffield, Robert E. Thurman, Lingyun Song, Alexias Safi, J Stamatoyannopoulos, Boris Lenhard, Gregory E. Crawford, Terrence S. Furey

    Published 2013
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  15. 15
    Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1

    Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1 by Eleni M. Tomazou, Nathan C. Sheffield, Christian Schmidl, Michael Schuster, Andreas Schönegger, Paul Datlinger, Stefan Kubicek, Christoph Bock, Heinrich Kovar

    Published 2015
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  16. 16
    Single-cell epigenomic variability reveals functional cancer heterogeneity

    Single-cell epigenomic variability reveals functional cancer heterogeneity by Ulrike Litzenburger, Jason D. Buenrostro, Beijing Wu, Ying Shen, Nathan C. Sheffield, Arwa S. Kathiria, William J. Greenleaf, Howard Y. Chang

    Published 2017
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  17. 17
    Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

    Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity by Alok K. Tewari, Galip Gürkan Yardımcı, Yoichiro Shibata, Nathan C. Sheffield, Lingyun Song, Barry S. Taylor, Stoyan Georgiev, Gerhard A. Coetzee, Uwe Ohler, Terrence S. Furey, Gregory E. Crawford, Phillip G. Febbo

    Published 2012
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  18. 18
    Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development

    Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development by Eliza Duvall, Cecil M. Benitez, Krissie Tellez, Martin Enge, Philip T. Pauerstein, Lingyu Li, Songjoon Baek, Stephen R. Quake, Jason P. Smith, Nathan C. Sheffield, Seung K. Kim, H. Efsun Arda

    Published 2022
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  19. 19
    Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

    Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection by Yoichiro Shibata, Nathan C. Sheffield, Olivier Fédrigo, Courtney C. Babbitt, Matthew Wortham, Alok K. Tewari, Darin London, Lingyun Song, Bum-Kyu Lee, Vishwanath R. Iyer, Stephen C. J. Parker, Elliott H. Margulies, Gregory A. Wray, Terrence S. Furey, Gregory E. Crawford

    Published 2012
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  20. 20
    Integrative Single-Cell Meta-Analysis Reveals Disease-Relevant Vascular Cell States and Markers in Human Atherosclerosis

    Integrative Single-Cell Meta-Analysis Reveals Disease-Relevant Vascular Cell States and Markers in Human Atherosclerosis by José Verdezoto Mosquera, Gaëlle Auguste, Doris C. Wong, Adam W. Turner, Chani J. Hodonsky, Christian Lino Cardenas, Konstantinos Theofilatos, Maxime M. Bos, Maryam Kavousi, Patricia A. Peyser, Manuel Mayr, Jason Kovacic, Johan Björkegren, Rajeev Malhotra, Sander W. van der Laan, Chongzhi Zang, Nathan C. Sheffield, Clint L. Miller

    Published 2023
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